The overall objective of this research is to develop an instrument for use in functional genomics and system biology that is capable of identifying and quantifying unlabeled macromolecules (proteins and nucleic acids) in complex mixtures. This system will identify the macromolecules in single molecule detection mode with a highly parallel detection format, thereby avoiding the loss of information associated with ensemble measurements while achieving statistically significant sample sizes to avoid spurious results. This system will be used with three different measurement settings: macromolecules in solution, macromolecules at the cell surface, and immobilized biochemistry platforms. This instrument is based on detecting interactions between the macromolecules and a newly invented photonics effect, SPEI. SPEI is a photonics effect that is capable to achieving high light transmission coefficients through an array of subwavelength apertures. These apertures are currently being fabricated with diameters of 50 nm and it is expected that diameters as small as 10 nm are possible. The hypothesis upon which this instrument development is based is that macromolecules will alter the emission of light from the array of apertures by changing the intensity of the emitted light or shifting the resonance of the array. These effects will create a unique signature that can be used to detect and quantify macromolecules at the single molecule level with statistically significant sample sizes. The research in the R21 phase will be focused on demonstrating the effects of these macromolecular interactions with SPEI and generating/identifying characteristic signatures. The research in the R33 phase will be focused on developing an instrument system that can control the flow of the macromolecules through the apertures and manipulate the biochemical and physical environments. This system will then be applied to the study of macromolecules in solution, cell surface phenomena, and immobilized biochemistry (e.g. protein microarrays).